Ignore Blank Values and Inactive Records in Duplicate Detection
This has been an issue, but with CRM roll up 5 this has been rectified.
If you want to do this and it’s not in your CRM 2011 then please check the roll up version. Only with CRM roll up version 5 this comes. However this roll up cannot be uninstalled.
Information about update roll up 5.
You can download the roll up version 5 from here.